MERFISH Report
1. Overview
Principle Investigator: Mehrdad Shamloo
Institution: Stanford
Project: SPR22-003 Aged Sleep Deprivation study
1.1 Slice Submission
This is the detailed slice information we got from collaborators:
| Sample ID | Anatomical source | Preparation method | Treatments | Species & Genetic background | Sex | Age |
|---|---|---|---|---|---|---|
| 1 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl6 | m | 18 mo |
| 2 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl7 | m | 18 mo |
| 3 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 18 months | mouse c57bl8 | m | 18 mo |
| 23 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl9 | m | 18 mo |
| 24 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl10 | m | 18 mo |
| 25 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 18 months | mouse c57bl11 | m | 18 mo |
| 31 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl12 | m | 4 mo |
| 32 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl13 | m | 4 mo |
| 33 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl14 | m | 4 mo |
| 34 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl15 | m | 4 mo |
| 35 | brain hemisphere | perfused and flash frozen in OCT embedding media | No Sleep Deprivation- 4 months | mouse c57bl16 | m | 4 mo |
| 36 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl17 | m | 4 mo |
| 37 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl18 | m | 4 mo |
| 38 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl19 | m | 4 mo |
| 39 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl20 | m | 4 mo |
| 40 | brain hemisphere | perfused and flash frozen in OCT embedding media | Sleep Deprivation- 4 months | mouse c57bl21 | m | 4 mo |
1.2 Sample Information
A brief sample information is generated from the submission table for the following analysis.
“SD” refers to “Sleep Deprivation” while “nSD” refers to “No Sleep Deprivation”.
| Batch | Index | Genotype | region | Mice Age (month) | Data Path |
|---|---|---|---|---|---|
| 1 | nSD1 | nSD | region_0 | 18 | 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101 |
| 1 | SD23 | SD | region_1 | 18 | 202310191044_20231019StanfordSD1n23VZG191m500x01_VMSC00101 |
| 2 | nSD2 | nSD | region_0 | 18 | 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201 |
| 2 | SD24 | SD | region_1 | 18 | 202311201155_20231120StanfordSD2n24VZG191m500x02_VMSC05201 |
| 3 | nSD3 | nSD | region_0 | 18 | 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201 |
| 3 | SD25 | SD | region_1 | 18 | 202312121344_20231212StanfordSD3n25VZG191x500x01_VMSC05201 |
| 4 | SD36 | SD | region_0 | 4 | 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101 |
| 4 | nSD31 | nSD | region_1 | 4 | 202312151433_20231215StanfordSD3136VZG191m500x4mx01_VMSC00101 |
| 5 | SD37 | SD | region_0 | 4 | 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101 |
| 5 | nSD32 | nSD | region_1 | 4 | 202312271640_20231227StanfordSD4m3237VZG191x500x02_VMSC00101 |
| 6 | SD38 | SD | region_0 | 4 | 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201 |
| 6 | nSD33 | nSD | region_1 | 4 | 202312271749_20231227Stanford4mSD3338VZG191x500x3_VMSC05201 |
1.3 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 5.0 in most area can be considered as a good quality standard.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
MERSCOPE Data Quality Summary
2. Data Processing & Analysis
2.1 Cell Segmentation
Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.
To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 1800], and the gene count per cell > 25. After filter the outliers, the qualified cells count is shown in the following table.
Outliers were filtered from the data, and the qualified cells count is presented in the following table. The identified cells after filtering are listed in the following table. In total, the study identified ** 712944** cells across 12 samples.
| Sample Index | Cell Count |
|---|---|
| SD36 | 66786 |
| SD24 | 65480 |
| nSD31 | 62351 |
| SD25 | 60474 |
| SD23 | 59687 |
| nSD3 | 58384 |
| nSD2 | 57578 |
| SD37 | 57423 |
| nSD32 | 56953 |
| nSD1 | 56686 |
| nSD33 | 56259 |
| SD38 | 54883 |
Identified Cell Spatial Overview on all Samples
2.2 Batch Effect & Dimension Reduction
We use Scanpy for the analysis of single-cell level transcriptome data. The initial stage of our analysis involves the elimination of batch effects, thereby ensuring that different samples from various batches are distributed within the same domain and are statistically reasonable to be integrated and compared. To achieve this, we utilize the Harmony algorithm.
Subsequently, we present visualizations of the batch difference by Leiden UMAP clusters. Also, we illustrate the distributions of the Leiden clusters for future analysis.
Transcript counts on each sample
Umap of cells and colored by batch
Umap of cells on each batch
Leiden Umap can be dividied to 28 clusters
2.3 Cell Annotation
We use a recent published tool: Map My Cell to perform cell type annotations for each cell. It is a high resolution cell type annotator build by Alan Institude, with nested levels of classification including 34 classes and 338 subclasses.
The taxonomy is based on the Allen Mouse Brain Common Coordinate Framework version 3 (CCFv3)[https://doi.org/10.1016/j.cell.2020.04.007]. Part of the used abbreviations is list in the supplementary Abbreviation. Otherwise can be found in CCFv3 paper.
With the annotation, we can identify and plot the selected types of cells in each sample.
2.3.1 Low Resolution Class
| class_name | count |
|---|---|
| 31 OPC-Oligo | 168524 |
| 30 Astro-Epen | 112863 |
| 33 Vascular | 80432 |
| 01 IT-ET Glut | 79488 |
| 09 CNU-LGE GABA | 46138 |
| 02 NP-CT-L6b Glut | 26178 |
| 19 MB Glut | 23711 |
| 20 MB GABA | 23531 |
| 34 Immune | 19905 |
| 12 HY GABA | 17968 |
| 18 TH Glut | 16273 |
| 27 MY GABA | 13050 |
| 11 CNU-HYa GABA | 12030 |
| 10 LSX GABA | 9649 |
| 07 CTX-MGE GABA | 8601 |
| 14 HY Glut | 8382 |
| 23 P Glut | 7868 |
| 26 P GABA | 6320 |
| 24 MY Glut | 5293 |
| 06 CTX-CGE GABA | 5004 |
| 08 CNU-MGE GABA | 4806 |
| 05 OB-IMN GABA | 4294 |
| 13 CNU-HYa Glut | 3073 |
| 32 OEC | 2658 |
| 04 DG-IMN Glut | 1602 |
| 21 MB Dopa | 1572 |
| 28 CB GABA | 1073 |
| 03 OB-CR Glut | 624 |
| 29 CB Glut | 529 |
| 17 MH-LH Glut | 524 |
| 22 MB-HB Sero | 516 |
| 16 HY MM Glut | 373 |
| 25 Pineal Glut | 57 |
| 15 HY Gnrh1 Glut | 35 |
2.3.2 High Resolution Class
| subclass_name | count | |
|---|---|---|
| 7 | 327 Oligo NN | 155504 |
| 3 | 333 Endo NN | 51244 |
| 11 | 318 Astro-NT NN | 42990 |
| 0 | 319 Astro-TE NN | 42944 |
| 183 | 062 STR D2 Gaba | 19098 |
| 12 | 334 Microglia NN | 17604 |
| 31 | 030 L6 CT CTX Glut | 17454 |
| 191 | 061 STR D1 Gaba | 16343 |
| 24 | 006 L4/5 IT CTX Glut | 15131 |
| 8 | 331 Peri NN | 14424 |
| 5 | 321 Astroependymal NN | 14038 |
| 2 | 326 OPC NN | 13020 |
| 219 | 151 TH Prkcd Grin2c Glut | 10526 |
| 20 | 004 L6 IT CTX Glut | 9409 |
| 17 | 007 L2/3 IT CTX Glut | 8913 |
| 146 | 181 IC Tfap2d Maf Glut | 8894 |
| 32 | 005 L5 IT CTX Glut | 8516 |
| 50 | 010 IT AON-TT-DP Glut | 8110 |
| 1 | 330 VLMC NN | 7734 |
| 18 | 009 L2/3 IT PIR-ENTl Glut | 6929 |
| 195 | 063 STR D1 Sema5a Gaba | 6476 |
| 130 | 323 Ependymal NN | 5675 |
| 9 | 332 SMC NN | 5206 |
| 44 | 022 L5 ET CTX Glut | 5082 |
| 60 | 020 L2/3 IT RSP Glut | 4968 |
| 26 | 052 Pvalb Gaba | 4876 |
| 46 | 285 MY Lhx1 Gly-Gaba | 4508 |
| 43 | 016 CA1-ProS Glut | 4380 |
| 59 | 101 ZI Pax6 Gaba | 3944 |
| 54 | 029 L6b CTX Glut | 3579 |
| 42 | 325 CHOR NN | 3337 |
| 30 | 053 Sst Gaba | 3146 |
| 40 | 069 LSX Nkx2-1 Gaba | 3131 |
| 62 | 032 L5 NP CTX Glut | 3123 |
| 78 | 093 RT-ZI Gnb3 Gaba | 2933 |
| 10 | 328 OEC NN | 2658 |
| 38 | 017 CA3 Glut | 2654 |
| 204 | 060 OT D3 Folh1 Gaba | 2452 |
| 180 | 235 PG-TRN-LRN Fat2 Glut | 2381 |
| 69 | 198 IC Six3 En2 Gaba | 2366 |
| 131 | 202 PRT Tcf7l2 Gaba | 2338 |
| 33 | 070 LSX Prdm12 Slit2 Gaba | 2262 |
| 76 | 098 AHN-SBPV-PVHd Pdrm12 Gaba | 2229 |
| 21 | 046 Vip Gaba | 2212 |
| 29 | 071 LSX Prdm12 Zeb2 Gaba | 2205 |
| 107 | 300 PARN-MDRNd-NTS Gbx2 Gly-Gaba | 2160 |
| 225 | 148 AV Col27a1 Glut | 2025 |
| 72 | 320 Astro-OLF NN | 1987 |
| 205 | 154 PF Fzd5 Glut | 1971 |
| 135 | 207 SCs Dmbx1 Gaba | 1829 |
| 4 | 329 ABC NN | 1824 |
| 52 | 201 PAG-RN Nkx2-2 Otx1 Gaba | 1794 |
| 141 | 205 SC-PAG Lef1 Emx2 Gaba | 1789 |
| 53 | 041 OB-in Frmd7 Gaba | 1778 |
| 260 | 129 VMH Nr5a1 Glut | 1776 |
| 118 | 057 NDB-SI-MA-STRv Lhx8 Gaba | 1753 |
| 167 | 243 PGRN-PARN-MDRN Hoxb5 Glut | 1702 |
| 85 | 306 SPVI-SPVC Sall3 Lhx1 Gly-Gaba | 1687 |
| 6 | 049 Lamp5 Gaba | 1648 |
| 271 | 104 TU-ARH Otp Six6 Gaba | 1634 |
| 273 | 215 SNc-VTA-RAmb Foxa1 Dopa | 1572 |
| 188 | 037 DG Glut | 1569 |
| 108 | 064 STR-PAL Chst9 Gaba | 1415 |
| 236 | 134 PH-ant-LHA Otp Bsx Glut | 1351 |
| 148 | 222 PB Evx2 Glut | 1343 |
| 138 | 213 SCsg Gabrr2 Gaba | 1340 |
| 82 | 304 NTS-PARN Neurod2 Gly-Gaba | 1314 |
| 77 | 195 SNr-VTA Pax5 Npas1 Gaba | 1278 |
| 34 | 338 Lymphoid NN | 1265 |
| 73 | 203 LGv-SPFp-SPFm Nkx2-2 Tcf7l2 Gaba | 1248 |
| 152 | 090 BST-MPN Six3 Nrgn Gaba | 1244 |
| 13 | 210 PRT Mecom Gaba | 1216 |
| 282 | 102 DMH-LHA Gsx1 Gaba | 1182 |
| 28 | 199 PAG-MRN-RN Foxa2 Gaba | 1171 |
| 105 | 209 SCs Pax7 Nfia Gaba | 1121 |
| 222 | 107 DMH Hmx2 Gaba | 1067 |
| 99 | 089 PVR Six3 Sox3 Gaba | 1064 |
| 192 | 081 ACB-BST-FS D1 Gaba | 1046 |
| 264 | 086 MPO-ADP Lhx8 Gaba | 1042 |
| 196 | 088 BST Tac2 Gaba | 1024 |
| 142 | 073 MEA-BST Sox6 Gaba | 1005 |
| 143 | 068 LSX Otx2 Gaba | 1004 |
| 215 | 106 PVpo-VMPO-MPN Hmx2 Gaba | 996 |
| 209 | 182 CUN-PPN Evx2 Meis2 Glut | 996 |
| 229 | 217 PB Lmx1a Glut | 987 |
| 74 | 200 PAG-ND-PCG Onecut1 Gaba | 981 |
| 137 | 187 SCsg Pde5a Glut | 959 |
| 171 | 176 SCig Foxb1 Glut | 955 |
| 93 | 002 IT EP-CLA Glut | 926 |
| 47 | 045 OB-STR-CTX Inh IMN | 922 |
| 23 | 047 Sncg Gaba | 919 |
| 102 | 056 Sst Chodl Gaba | 909 |
| 147 | 119 SI-MA-LPO-LHA Skor1 Glut | 895 |
| 90 | 264 PRNc Otp Gly-Gaba | 894 |
| 70 | 322 Tanycyte NN | 893 |
| 56 | 251 NTS Dbh Glut | 865 |
| 144 | 085 SI-MPO-LPO Lhx8 Gaba | 864 |
| 79 | 317 Astro-CB NN | 860 |
| 139 | 208 SC Lef1 Otx2 Gaba | 857 |
| 217 | 168 SPA-SPFm-SPFp-POL-PIL-PoT Sp9 Glut | 854 |
| 155 | 177 SCig-an-PPT Foxb1 Glut | 850 |
| 88 | 076 MEA-BST Lhx6 Nfib Gaba | 848 |
| 216 | 100 AHN Onecut3 Gaba | 837 |
| 227 | 224 PCG-PRNr Vsx2 Nkx6-1 Glut | 830 |
| 66 | 033 NP SUB Glut | 826 |
| 110 | 054 STR Prox1 Lhx6 Gaba | 825 |
| 169 | 180 SCiw Pitx2 Glut | 824 |
| 226 | 164 APN C1ql4 Glut | 812 |
| 124 | 147 AD Serpinb7 Glut | 774 |
| 207 | 173 PAG Pou4f2 Glut | 773 |
| 101 | 039 OB Meis2 Thsd7b Gaba | 769 |
| 91 | 221 LDT-PCG Vsx2 Lhx4 Glut | 747 |
| 133 | 212 SCs Lef1 Gli3 Gaba | 746 |
| 116 | 103 PVHd-DMH Lhx6 Gaba | 744 |
| 114 | 025 CA2-FC-IG Glut | 742 |
| 81 | 267 CS-PRNr-PCG Tmem163 Otp Gaba | 739 |
| 87 | 021 L4 RSP-ACA Glut | 728 |
| 157 | 172 PAG Pou4f1 Ebf2 Glut | 722 |
| 281 | 074 MEA-BST Lhx6 Sp9 Gaba | 721 |
| 193 | 058 PAL-STR Gaba-Chol | 721 |
| 250 | 132 AHN-RCH-LHA Otp Fezf1 Glut | 706 |
| 194 | 079 CEA-BST Six3 Cyp26b1 Gaba | 702 |
| 14 | 337 DC NN | 677 |
| 182 | 278 NLL Gata3 Gly-Gaba | 670 |
| 159 | 162 CUN Evx2 Lhx2 Glut | 655 |
| 92 | 072 LSX Sall3 Lmo1 Gaba | 655 |
| 49 | 283 PRP Otp Gly-Gaba | 642 |
| 249 | 108 ARH-PVp Tbx3 Gaba | 639 |
| 104 | 196 PAG-PPN Pax5 Sox21 Gaba | 638 |
| 96 | 265 PB Sst Gly-Gaba | 625 |
| 267 | 082 CEA-BST Ebf1 Pdyn Gaba | 611 |
| 22 | 192 PPN-CUN-PCG Otp En1 Gaba | 604 |
| 198 | 055 STR Lhx8 Gaba | 598 |
| 83 | 270 LDT-DTN Gata3 Nfix Gaba | 591 |
| 75 | 023 SUB-ProS Glut | 583 |
| 165 | 238 NTS Phox2b Glut | 574 |
| 95 | 027 L6b EPd Glut | 568 |
| 311 | 128 VMH Fezf1 Glut | 557 |
| 36 | 305 SPVI-SPVC Sall3 Nfib Gly-Gaba | 551 |
| 224 | 163 APN C1ql2 Glut | 544 |
| 223 | 150 CM-IAD-CL-PCN Sema5b Glut | 543 |
| 181 | 175 SC Bnc2 Glut | 538 |
| 154 | 169 PAG-SC Pou4f1 Zic1 Glut | 531 |
| 48 | 003 L5/6 IT TPE-ENT Glut | 520 |
| 235 | 216 MB-MY Tph2 Glut-Sero | 516 |
| 51 | 277 DTN-LDT-IPN Otp Pax3 Gaba | 515 |
| 201 | 161 PAG Pou4f3 Glut | 507 |
| 27 | 019 L2/3 IT PPP Glut | 490 |
| 203 | 268 CS-PRNr-DR En1 Sox2 Gaba | 485 |
| 239 | 080 CEA-AAA-BST Six3 Sp9 Gaba | 485 |
| 261 | 124 MPN-MPO-PVpo Hmx2 Glut | 478 |
| 160 | 174 PAG Pou4f2 Mesi2 Glut | 476 |
| 248 | 133 PVH-SO-PVa Otp Glut | 471 |
| 240 | 094 SCH Six6 Cdc14a Gaba | 461 |
| 149 | 146 LH Pou4f1 Sox1 Glut | 446 |
| 120 | 035 OB Eomes Ms4a15 Glut | 424 |
| 156 | 170 PAG-MRN Tfap2b Glut | 418 |
| 258 | 311 CBX MLI Megf11 Gaba | 414 |
| 125 | 042 OB-out Frmd7 Gaba | 405 |
| 35 | 028 L6b/CT ENT Glut | 403 |
| 128 | 197 SNr Six3 Gaba | 402 |
| 158 | 171 PAG Pou4f1 Bnc2 Glut | 399 |
| 202 | 067 LSX Sall3 Pax6 Gaba | 392 |
| 136 | 211 SC Tnnt1 Gli3 Gaba | 384 |
| 134 | 139 PH-LHA Foxb1 Glut | 380 |
| 212 | 166 MRN Pou3f1 C1ql4 Glut | 379 |
| 305 | 136 PMv-TMv Pitx2 Glut | 375 |
| 161 | 167 PRC-PAG Tcf7l2 Irx2 Glut | 375 |
| 283 | 135 STN-PSTN Pitx2 Glut | 367 |
| 61 | 194 MRN-VTN-PPN Pax5 Cdh23 Gaba | 363 |
| 16 | 263 CS-RPO Meis2 Gaba | 359 |
| 173 | 206 SCm-PAG Cdh23 Gaba | 355 |
| 151 | 083 CEA-BST Rai14 Pdyn Crh Gaba | 354 |
| 19 | 018 L2 IT PPP-APr Glut | 352 |
| 163 | 160 PAG-SC Neurod2 Meis2 Glut | 351 |
| 279 | 111 TRS-BAC Sln Glut | 344 |
| 71 | 299 MARN-PPY Ngfr Gly-Gaba | 341 |
| 15 | 271 NI-RPO Gata3 Nr4a2 Gaba | 338 |
| 295 | 117 LHA Barhl2 Glut | 333 |
| 213 | 193 MRN-PPN-CUN Pax8 Gaba | 331 |
| 132 | 066 NDB-SI-ant Prdm12 Gaba | 326 |
| 244 | 110 BST-po Iigp1 Glut | 320 |
| 140 | 246 CU-ECU-SPVI Foxb1 Glut | 320 |
| 247 | 141 PH-SUM Foxa1 Glut | 319 |
| 127 | 254 VCO Mafa Meis2 Glut | 319 |
| 208 | 144 MM Foxb1 Glut | 316 |
| 106 | 051 Pvalb chandelier Gaba | 306 |
| 164 | 245 SPVI-SPVC Tlx3 Ebf3 Glut | 306 |
| 129 | 087 MPN-MPO-LPO Lhx6 Zfhx3 Gaba | 302 |
| 64 | 272 LDT-PCG-CS Gata3 Lhx1 Gaba | 302 |
| 175 | 188 SCop Sln Glut | 296 |
| 231 | 165 PAG-MRN Pou3f1 Glut | 290 |
| 189 | 013 COAp Grxcr2 Glut | 284 |
| 200 | 092 TMv-PMv Tbx3 Hist-Gaba | 283 |
| 55 | 314 CB Granule Glut | 280 |
| 179 | 140 PMd-LHA Foxb1 Glut | 280 |
| 199 | 126 ARH-PVp Tbx3 Glut | 276 |
| 296 | 097 PVHd-SBPV Six3 Prox1 Gaba | 275 |
| 25 | 050 Lamp5 Lhx6 Gaba | 273 |
| 57 | 229 PB-NTS Phox2b Ebf3 Lmx1b Glut | 270 |
| 109 | 012 MEA Slc17a7 Glut | 268 |
| 252 | 115 MS-SF Bsx Glut | 264 |
| 115 | 335 BAM NN | 258 |
| 100 | 315 DCO UBC Glut | 249 |
| 303 | 125 DMH Hmx2 Glut | 248 |
| 103 | 044 OB Dopa-Gaba | 246 |
| 170 | 220 PB Pax5 Glut | 245 |
| 302 | 127 DMH-LHA Vgll2 Glut | 244 |
| 277 | 155 PRC-PAG Pax6 Glut | 242 |
| 245 | 152 RE-Xi Nox4 Glut | 238 |
| 98 | 313 CBX Purkinje Gaba | 237 |
| 185 | 099 SBPV-PVa Six6 Satb2 Gaba | 235 |
| 293 | 131 LHA-AHN-PVH Otp Trh Glut | 230 |
| 232 | 287 MV-SPIV-PRP Dmbx1 Gly-Gaba | 228 |
| 290 | 118 ADP-MPO Trp73 Glut | 227 |
| 122 | 048 RHP-COA Ndnf Gaba | 225 |
| 176 | 105 TMd-DMH Foxd2 Gaba | 223 |
| 162 | 237 PRP-NI-PRNc-GRN Otp Glut | 212 |
| 197 | 225 PRNc-NI-SG-RPO Vsx2 Nr4a2 Glut | 209 |
| 174 | 279 PSV Pax2 Gly-Gaba | 205 |
| 187 | 114 COAa-PAA-MEA Barhl2 Glut | 204 |
| 119 | 290 MY Prox1 Lmo7 Gly-Gaba | 203 |
| 126 | 036 HPF CR Glut | 200 |
| 177 | 261 HB Calcb Chol | 197 |
| 238 | 109 LGv-ZI Otx2 Gaba | 197 |
| 270 | 231 IPN-LDT Vsx2 Nkx6-1 Glut | 189 |
| 145 | 257 SPVC Ccdc172 Glut | 188 |
| 246 | 156 MB-ant-ve Dmrta2 Glut | 184 |
| 41 | 293 PAS-MV Ebf2 Gly-Gaba | 184 |
| 58 | 308 DCO Il22 Gly-Gaba | 182 |
| 113 | 059 GPe-SI Sox6 Cyp26b1 Gaba | 181 |
| 269 | 248 MV-SPIV Zic4 Neurod2 Glut | 179 |
| 45 | 065 IA Mgp Gaba | 173 |
| 287 | 223 B-PB Nr4a2 Glut | 172 |
| 84 | 214 IPN Otp Crisp1 Gaba | 166 |
| 326 | 292 MV Nkx6-1 Gly-Gaba | 165 |
| 298 | 276 LDT-PCG St18 Gaba | 164 |
| 39 | 008 L2/3 IT ENT Glut | 157 |
| 166 | 149 PVT-PT Ntrk1 Glut | 148 |
| 67 | 204 SC Otx2 Gcnt4 Gaba | 145 |
| 309 | 116 AVPV-MEPO-SFO Tbr1 Glut | 140 |
| 153 | 303 IRN Dmbx1 Pax2 Gly-Gaba | 138 |
| 172 | 186 SCop Pou4f2 Neurod2 Glut | 136 |
| 63 | 273 PDTg-PCG Pax6 Gaba | 130 |
| 186 | 228 PSV Pvalb Lhx2 Glut | 130 |
| 285 | 294 MV Pax6 Gly-Gaba | 127 |
| 168 | 178 SCig Foxb1 Otx2 Glut | 125 |
| 297 | 130 LHA Pmch Glut | 124 |
| 117 | 034 NP PPP Glut | 123 |
| 86 | 043 OB-mi Frmd7 Gaba | 118 |
| 286 | 282 POR Spp1 Gly-Gaba | 117 |
| 265 | 288 MDRN Hoxb5 Ebf2 Gly-Gaba | 116 |
| 254 | 179 SCdg-PAG Tfap2b Glut | 114 |
| 278 | 284 GRN-IRN-MDRNd Ikzf1 Gly-Gaba | 114 |
| 259 | 316 Bergmann NN | 113 |
| 292 | 084 BST-SI-AAA Six3 Slc22a3 Gaba | 113 |
| 230 | 298 PRP Gata3 Slc6a5 Gly-Gaba | 112 |
| 294 | 121 MEA-BST Otp Zic2 Glut | 111 |
| 210 | 309 CB PLI Gly-Gaba | 110 |
| 221 | 113 MEA-COA-BMA Ccdc42 Glut | 109 |
| 228 | 233 NLL-SOC Spp1 Glut | 108 |
| 184 | 296 RPA Pax6 Hoxb5 Gly-Gaba | 108 |
| 178 | 185 SCig Tfap2b Chrnb3 Glut | 103 |
| 262 | 159 IF-RL-CLI-PAG Foxa1 Glut | 102 |
| 68 | 031 CT SUB Glut | 102 |
| 220 | 226 PRNc-PARN Tlx1 Glut | 102 |
| 65 | 336 Monocytes NN | 101 |
| 251 | 078 SI-MA-ACB Ebf1 Bnc2 Gaba | 100 |
| 313 | 312 CBX MLI Cdh22 Gaba | 100 |
| 214 | 247 MV-SPIV Phox2b Ebf3 Lbx1 Glut | 99 |
| 233 | 234 MEV Ppp1r1c Glut | 96 |
| 111 | 075 MEA-BST Lhx6 Nr2e1 Gaba | 95 |
| 37 | 014 LA-BLA-BMA-PA Glut | 95 |
| 256 | 138 PH Pitx2 Glut | 95 |
| 94 | 011 L2 IT ENT-po Glut | 93 |
| 234 | 286 PPY-PGRNl Vip Glyc-Gaba | 90 |
| 268 | 077 CEA-BST Gal Avp Gaba | 84 |
| 206 | 157 RN Spp1 Glut | 82 |
| 315 | 145 MH Tac2 Glut | 78 |
| 263 | 281 POR Gata3 Gly-Gaba | 74 |
| 211 | 123 DMH Nkx2-4 Glut | 73 |
| 314 | 297 CU-ECU Pax2 Gly-Gaba | 71 |
| 266 | 191 PAG-MRN Rln3 Gaba | 69 |
| 317 | 232 LDT Vsx2 Nkx6-1 Nfib Glut | 68 |
| 80 | 001 CLA-EPd-CTX Car3 Glut | 68 |
| 237 | 291 NTS-MDRNd Prox1 Zic1 Gly-Gaba | 67 |
| 308 | 122 LHA-MEA Otp Glut | 65 |
| 253 | 256 SPVC Mafa Glut | 65 |
| 310 | 252 DMX VII Tbx20 Chol | 63 |
| 190 | 015 ENTmv-PA-COAp Glut | 61 |
| 112 | 302 MV Xdh Gly-Gaba | 60 |
| 306 | 143 MM-ant Foxb1 Glut | 57 |
| 243 | 262 Pineal Crx Glut | 57 |
| 97 | 040 OB Trdn Gaba | 56 |
| 257 | 158 MRN-PAG Nkx6-1 Glut | 54 |
| 307 | 230 PRNr Otp Nfib Glut | 53 |
| 150 | 153 MG-POL-SGN Nts Glut | 48 |
| 280 | 091 ARH-PVi Six6 Dopa-Gaba | 47 |
| 323 | 269 LDT Fgf7 Gaba | 47 |
| 218 | 190 ND-INC Foxd2 Glut | 45 |
| 241 | 275 PDTg Otp Olig3 Gaba | 42 |
| 274 | 250 CBN Neurod2 Pvalb Glut | 39 |
| 334 | 253 IO Fgl2 Glut | 38 |
| 332 | 112 GPi Tbr1 Cngb3 Gaba-Glut | 37 |
| 291 | 142 HY Gnrh1 Glut | 35 |
| 242 | 038 DG-PIR Ex IMN | 33 |
| 321 | 137 PH-an Pitx2 Glut | 32 |
| 316 | 244 MV-SPIV Slc6a2 Glut | 32 |
| 330 | 096 PVHd Gsc Gaba | 31 |
| 304 | 310 CBX Golgi Gly-Gaba | 30 |
| 319 | 324 Hypendymal NN | 26 |
| 301 | 184 PAG Tcf24 Glut | 26 |
| 123 | 307 RO-RPA Pkd2l1 Gaba | 25 |
| 300 | 120 MEA Otp Foxp2 Glut | 24 |
| 288 | 026 NLOT Rho Glut | 23 |
| 276 | 255 SPVO Mafa Meis2 Glut | 20 |
| 299 | 218 PSV Lmx1a Trpv6 Glut | 19 |
| 327 | 239 MARN-GRN Pyy Glut | 19 |
| 275 | 295 CBN Dmbx1 Gaba | 19 |
| 329 | 236 IRN Vip Glut | 16 |
| 272 | 258 SPVC Nmu Glut | 13 |
| 255 | 289 MDRNd Prox1 Pax6 Gly-Gaba | 13 |
| 324 | 274 PDTg Otp Shroom3 Gaba | 12 |
| 322 | 242 PGRNd Dmbx1 Glut | 12 |
| 289 | 095 DMH Prdm13 Gaba | 11 |
| 333 | 266 PRNc Prox1 Brs3 Gly-Gaba | 9 |
| 318 | 227 PB-PSV Phox2b Glut | 8 |
| 312 | 301 MV Nr4a2 Gly-Gaba | 7 |
| 284 | 219 PB-SUT Tlx3 Lhx2 Glut | 7 |
| 331 | 240 MDRNv Lhx4 Qrfprl Glut | 7 |
| 89 | 024 L5 PPP Glut | 6 |
| 328 | 249 NTS Aldh1a2 Glut | 6 |
| 325 | 189 PAG Ucn Glut | 3 |
| 320 | 260 MDRNv Crp Glut | 2 |
| 121 | 280 NLL-po Pax7 Gaba | 2 |
| 335 | 183 PBG Mtnr1a Glut-Chol | 1 |
2.3.3 Selected Cell Class
| select_class_name | count | |
|---|---|---|
| 1 | Astrocyte | 96912 |
| 2 | Endo | 50134 |
| 9 | L6b Glut | 21511 |
| 5 | L2/3 Glut | 20604 |
| 3 | Microglia | 17253 |
| 10 | L5 Glut | 16403 |
| 19 | TH Glut | 15993 |
| 8 | L4/5 Glut | 14734 |
| 11 | MY GABA | 12482 |
| 7 | L6 Glut | 9129 |
| 14 | P Glut | 7729 |
| 4 | P GABA | 6187 |
| 18 | MY Glut | 5163 |
| 17 | CA1 Glut | 4268 |
| 12 | CA3 Glut | 2579 |
| 20 | DG Glut | 1548 |
| 16 | CA2 Glut | 717 |
| 15 | L4 Glut | 698 |
| 13 | L5/6 Glut | 505 |
| 6 | L2 Glut | 438 |
2.3.4 Selected Cell Type Umap
2.3.4 Selected Cell Type Spatial Map
2.3.5 Selected Cell Type Proportion
3. Manual Region Selection
Manual selection mostly based on the cell type annotation.
3.1 Hippocampus
3.2 Frontal Cortex
3.3 Locus ceruleus (Unfinished!)
To find LC region, we tries to show LC marker gene expression: Th, Dbh.
Th Gene Spatial Map